[Chimera-users] How to show hydrophobility clearly

[Kenji MATSUI]

Dear  Elaine

Thank you for your reply.

I now know that I have to try it the way you taught me before.

I will try to adjust it again.

Thank you very much for your kind replies.
---------------------------------------------------------------------------
松井 健治
 東京農工大学大学院 工学府産業技術専攻 修士 2年
〒184-8588 東京都小金井市中町2-24-16
 Mail: s214903z at st.go.tuat.ac.jp

Kenji Matsui
 Graduate School of Tokyo University of Agriculture and Technology M2
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
 Mail: s214903z at st.go.tuat.ac.jp


2022年7月28日(木) 0:46 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Kenji
> In this latest message, you are using one method that shows the pocket
> surface only, like in the tutorial.  Your image after step 1 of what you
> tried looks OK to me:
> [image: 1edf41f0-9f2e-4921-92fe-19399979fd97.png]
>  But if you are not happy with that, I am guessing you do not want this
> method.
>
>  If you want it to look more like this example image with the labeling
> "hydrophobic pocket" and "allosteric tunnel"
>
>
>
> ...then you need to use a DIFFERENT method that includes clipping:
> showing the whole surface of the protein and then using clipping to slice.
>
>
> We already discussed this method, and you were already using this method
> the first time you asked the question:
> <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018741.html>
> <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018746.html>
>
> With that method, all you can do is to move and rotate the structure and
> move the clipping (either global clipping plane with Side View tool or
> surface-only clipping with Per-Model Clipping, both mentioned in previous
> replies) to try to get a good view.  However, different pockets are
> different shapes and depending on the shape of your pocket it may not be
> possible to make an image that clearly shows what you want.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jul 26, 2022, at 6:40 PM, Kenji MATSUI <s214903z at st.go.tuat.ac.jp>
> wrote:
>
> Dear Chimera
>
> Thank you for taking the time to answer my question the other day.
>
> I'm Kenji Matsui, a second-year master's student at a national university
> in Japan.
>
> I am looking at ligand-protein interactions and how they affect binding
> affinity.
>
> Therefore, I would like to examine the hydrophobicity and hydrophilicity
> around the ligand in the figure(third)
>
> If you know of any, could you please let us know?
>
> I tried to show what you mentioned in your email.(clip off, mclip)
>
> I apologize for asking this question so often in your busy schedule, but I
> would appreciate it if you could confirm it for me.
>
> <image.png>   <image.png>
>
> The picture I want to show
> <image.png>
>
> Tried thing
> 1. clip off +~ribbon
> <1edf41f0-9f2e-4921-92fe-19399979fd97.png>
>
> 2.m clip
> <image1.png>
>
>
>
>
> .
> ---------------------------------------------------------------------------
>
>
> Kenji Matsui
>  Graduate School of Tokyo University of Agriculture and Technology M2
> 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
>  Mail: s214903z at st.go.tuat.ac.jp
> <Hydrohobility_1P8D_LXR_LBD_mono_24,25-epoxycholesterol.pyc>
>
>
>
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